Plastome Rearrangements in the “Adenocalymma-Neojobertia” Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications

Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

(2016) Mario Vallejo-Marín et al.   AMERICAN JOURNAL OF BOTANY

Large-Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes)

(2016) Chung-Shien Wu et al.   Genome Biology and Evolution

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

(2016) Michelle Kendall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

(2016) Andrew G. Gardner et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses

(2016) Yanjun Zhang et al.   Frontiers in Plant Science

Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species

(2016) Sajjad Asaf et al.   Frontiers in Plant Science

Chloroplast Sequence of Treegourd (Crescentia cujete, Bignoniaceae) to Study Phylogeography and Domestication

(2016) Priscila Ambrósio Moreira et al.   Applications in Plant Sciences

Complete plastid genome sequence ofPrimula sinensis(Primulaceae): structure comparison, sequence variation and evidence foraccDtransfer to nucleus

(2016) Tong-Jian Liu et al.   PeerJ

The first complete plastid genomes of Melastomataceae are highly structurally conserved

(2016) Marcelo Reginato et al.   PeerJ

Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics

(2016) Nicola Harrison et al.   PLoS One

Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis

(2015) William P Wysocki et al.   BMC EVOLUTIONARY BIOLOGY

Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats

(2015) Shiliang Hu et al.   BMC GENOMICS

Biogeography and evolution ofDolichandra(Bignonieae, Bignoniaceae)

(2015) Luiz Henrique Martins Fonseca et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion

(2015) Chung-Shien Wu et al.   Genome Biology and Evolution

Phylogeny and biogeography of Tynanthus Miers (Bignonieae, Bignoniaceae)

(2015) Maria Cláudia M.P. de Medeiros et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

(2015) David Roy Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions

(2015) Stephen R. Downie et al.   SYSTEMATIC BOTANY

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

(2015) Diana V. Dugas et al.   Scientific Reports

Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome

(2015) Alison Gonçalves Nazareno et al.   PLoS One

A priori assessment of data quality in molecular phylogenetics

(2014) Bernhard Misof et al.   Algorithms for Molecular Biology

A New Generic Classification of Tribe Bignonieae (Bignoniaceae)1

(2014) Lúcia G. Lohmann et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

(2014) Peng-Fei Ma et al.   SYSTEMATIC BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

(2012) Dong-Keun Yi et al.   PLoS One

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Chloroplast genomes of photosynthetic eukaryotes

(2011) Beverley R. Green   PLANT JOURNAL

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Complete Plastid Genome Sequences of Three Rosids (Castanea, Prunus, Theobroma): Evidence for At Least Two Independent Transfers of rpl22 to the Nucleus

(2010) R. K. Jansen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage

(2010) M. M. Guisinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A molecular phylogeny and classification of Bignoniaceae

(2009) Richard G. Olmstead et al.   AMERICAN JOURNAL OF BOTANY

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH